Abstract
Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or disable expression of the gene. Whereas the known DNA and RNA binding proteins range in the thousands, only a few motifs have been examined. In this study, we have predicted putative regulatory motifs in groups of untranslated regions from genes regulated at the translational level in Arabidopsis thaliana under normal and stressed conditions. The test group of sequences was divided into random subgroups and subjected to three de novo motif finding algorithms (Seeder, Weeder and MEME). In addition to identifying sequence motifs, using an in silico tool we have predicted microRNA target sites in the 3′ UTRs of the translationally regulated genes, as well as identified upstream open reading frames located in the 5′ UTRs. Our bioinformatics strategy and the knowledge generated contribute to understanding gene regulation during stress, and can be applied to disease and stress resistant plant development.
Highlights
Precise regulation of gene expression is important for plants to survive environmental variations
The results show that approximately 19% (89/455) of the genes contain one or more upstream open reading frames (uORFs)
In order to understand the role of uORFs during gene translation under stress, several uORFs were detected in the 5′untranslated regions (UTRs) of translationally regulated genes expressed under stress
Summary
Precise regulation of gene expression is important for plants to survive environmental variations. Several features of mRNA influence the translation activity, most importantly regulatory elements in the 5′and 3′untranslated regions such as a 5′methyl cap and a 3′poly-A tail, which have both been found to play a significant role in regulating gene expression at the translational level[2,3,4]. An Arabidopsis SPL3 gene encoding an SBP-box transcription factor is translationally regulated by miR156/miR157, which inhibits SPL3 gene expression by binding to its target complementary site in the 3′UTR leading to early flowering phenotype[16]. It was discovered that a Bruno-like protein binds to a sequence element in the 3′UTR of SOC1 mRNA and represses its expression, thereby causing delayed flowering time[17]. In this study we set out to use various bioinformatics approaches and different computational tools to analyze genes that are translationally regulated under stress in Arabidopsis for various regulatory elements potentially responsible for mediating translational regulation
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